I think it is still hard to beat lsq_imp as implemented in 'O'. http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_e-l.html#anchor1342614
Cheers, Martin On Nov 15, 2010, at 2:32 AM, Clement Angkawidjaja wrote: > DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the > pairwise alignment function. It is all automatic and will give you the lowest > rmsd. Note, however, that it will omit parts that are very different for > calculation. > > Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the > residues you want to use for calculation for the lsq fit function. > > Regards, > Clement Angkawidjaja, PhD > Specially Appointed CMP Assistant Professor > Graduate School of Engineering > Osaka University > 2-1 Yamadaoka GSE Commoon East 8F > Suita-shi, Osaka 565-0871, Japan > Tel/Fax +81-6-6879-4580 > http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html > /////////////////////////////////////////////// > G30 Chemistry/Biology Combined Major Program > http://cmp.sci.osaka-u.ac.jp/CMP/ > > -----Original Message----- From: E rajakumar > Sent: Monday, November 15, 2010 6:52 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Question on calculation of RMSD > > Dear All > I have two structures of homo-dimeric protein complex with different DNA. > I want to calculate RMS deviation between second monomer from these two > complexes by fixing superposed first monomer. > > This I require to know what is the effect of DNA on relative orientation of > two monomers in the dimer. > > Previously I was using MOLEMAN2 to do this calculation. > > Please can you suggest me any other program to do this calculation. > > Thanking you > Raj > > > E. Rajakumara > Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering > Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 > (Mobile)
